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          <td width="10%" class="headerItem">Current view:</td>
          <td width="35%" class="headerValue"><a href="../../../../../../../../index.html">directory</a> - <a href="index.html">home/andres/Programacion/aso_coverage/aso/src/ASO/framework</a> - main.cpp (source / <a href="main.cpp.func.html">functions</a>)</td>
          <td width="10%"></td>
          <td width="10%" class="headerCovTableHead">Found</td>
          <td width="10%" class="headerCovTableHead">Hit</td>
          <td width="15%" class="headerCovTableHead">Coverage</td>
          <td width="5%"></td>
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          <td></td>
          <td class="headerItem">Test:</td>
          <td class="headerValue">cover.info</td>
          <td class="headerItem">Lines:</td>
          <td class="headerCovTableEntry">92</td>
          <td class="headerCovTableEntry">92</td>
          <td class="headerCovTableEntryHi">100.0 %</td>
        </tr>
        <tr>
          <td></td>
          <td class="headerItem">Date:</td>
          <td class="headerValue">2010-08-03</td>
          <td class="headerItem">Functions:</td>
          <td class="headerCovTableEntry">13</td>
          <td class="headerCovTableEntry">8</td>
          <td class="headerCovTableEntryLo">61.5 %</td>
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      <td><pre class="source">
<a name="1"><span class="lineNum">       1 </span>                : /**</a>
<span class="lineNum">       2 </span>                :  * \file  main.cpp
<span class="lineNum">       3 </span>                :  * \brief Main Program.
<span class="lineNum">       4 </span>                :  *
<span class="lineNum">       5 </span>                :  * ASO: Antiviral Sequence Optimizer
<span class="lineNum">       6 </span>                :  * &lt;http://aso.googlecode.com/&gt;
<span class="lineNum">       7 </span>                :  * Copyright (C) 2010 Velez Ezequiel, Peralta Andres, FuDePAN
<span class="lineNum">       8 </span>                :  *
<span class="lineNum">       9 </span>                :  * This file is part of the ASO project.
<span class="lineNum">      10 </span>                :  *
<span class="lineNum">      11 </span>                :  * Contents:      CPP file for ASO Main Program.
<span class="lineNum">      12 </span>                :  *
<span class="lineNum">      13 </span>                :  * System:         ASO
<span class="lineNum">      14 </span>                :  * Language:       C++
<span class="lineNum">      15 </span>                :  *
<span class="lineNum">      16 </span>                :  * Author:         Velez Ezequiel, Peralta Andres
<span class="lineNum">      17 </span>                :  * E-Mail:
<span class="lineNum">      18 </span>                :  *
<span class="lineNum">      19 </span>                :  * ASO is free software: you can redistribute it and/or modify
<span class="lineNum">      20 </span>                :  * it under the terms of the GNU General Public License as published by
<span class="lineNum">      21 </span>                :  * the Free Software Foundation, either version 3 of the License, or
<span class="lineNum">      22 </span>                :  * (at your option) any later version.
<span class="lineNum">      23 </span>                :  *
<span class="lineNum">      24 </span>                :  * ASO is distributed in the hope that it will be useful,
<span class="lineNum">      25 </span>                :  * but WITHOUT ANY WARRANTY; without even the implied warranty of
<span class="lineNum">      26 </span>                :  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
<span class="lineNum">      27 </span>                :  * GNU General Public License for more details.
<span class="lineNum">      28 </span>                :  *
<span class="lineNum">      29 </span>                :  * You should have received a copy of the GNU General Public License
<span class="lineNum">      30 </span>                :  * along with ASO.  If not, see &lt;http://www.gnu.org/licenses/&gt;.
<span class="lineNum">      31 </span>                :  *
<span class="lineNum">      32 </span>                :  */
<span class="lineNum">      33 </span>                : 
<span class="lineNum">      34 </span>                : #include &quot;gui_params.h&quot;
<span class="lineNum">      35 </span>                : 
<a name="36"><span class="lineNum">      36 </span>                : </a>
<span class="lineNum">      37 </span>                : struct O: public CombinationObserver
<a name="38"><span class="lineNum">      38 </span><span class="lineCov">              2 : {</span></a>
<span class="lineNum">      39 </span>                :      /*! Actualizar el Observador de Combinaciones */
<span class="lineNum">      40 </span><span class="lineCov">            485 :     inline bool update(const Avs* comb)</span>
<span class="lineNum">      41 </span>                :     {
<span class="lineNum">      42 </span><span class="lineCov">            485 :         CAutonomousIterator&lt;Avs&gt; Ait (*comb);</span>
<span class="lineNum">      43 </span><span class="lineCov">            485 :                 while(!Ait.end())</span>
<span class="lineNum">      44 </span>                :                 {
<span class="lineNum">      45 </span><span class="lineCov">           1395 :                     size_t id = 0;</span>
<span class="lineNum">      46 </span><span class="lineCov">           1395 :                         (*Ait)-&gt;get_attrib(&quot;id&quot;, id);</span>
<span class="lineNum">      47 </span><span class="lineCov">           1395 :                         std::cout &lt;&lt; id &lt;&lt; &quot;|&quot;;</span>
<span class="lineNum">      48 </span><span class="lineCov">           1395 :                         ++Ait;</span>
<span class="lineNum">      49 </span>                :                 }
<span class="lineNum">      50 </span><span class="lineCov">            485 :         std::cout&lt;&lt;std::endl;</span>
<span class="lineNum">      51 </span><span class="lineCov">            485 :         return true;</span>
<span class="lineNum">      52 </span>                :     }
<span class="lineNum">      53 </span>                : };
<a name="54"><span class="lineNum">      54 </span>                : </a>
<a name="55"><span class="lineNum">      55 </span>                : struct OI : public Observer&lt;int&gt;</a>
<span class="lineNum">      56 </span><span class="lineCov">              2 : {</span>
<span class="lineNum">      57 </span><span class="lineCov">              1 :         inline void update(const int* comb)</span>
<span class="lineNum">      58 </span>                :         {
<span class="lineNum">      59 </span>                :             
<span class="lineNum">      60 </span><span class="lineCov">              1 :         }</span>
<a name="61"><span class="lineNum">      61 </span>                : };</a>
<span class="lineNum">      62 </span>                : 
<span class="lineNum">      63 </span><span class="lineCov">              1 : int main(int argc, char **argv)</span>
<span class="lineNum">      64 </span>                : {
<span class="lineNum">      65 </span><span class="lineCov">              1 :     int TOTAL_PARAMS = 5;</span>
<span class="lineNum">      66 </span><span class="lineCov">              1 :     AntiviralSet antiviralSet;</span>
<span class="lineNum">      67 </span><span class="lineCov">              1 :     NucSequence nucSeq;</span>
<span class="lineNum">      68 </span>                : 
<span class="lineNum">      69 </span>                :     /*! Mostrar la ayuda. */
<span class="lineNum">      70 </span><span class="lineCov">              1 :     if (to_string(argv[1]) == &quot;--help&quot;)</span>
<span class="lineNum">      71 </span>                :     {
<span class="lineNum">      72 </span>                :         //gui_help(&quot;aso.help&quot;);
<span class="lineNum">      73 </span>                :     }
<span class="lineNum">      74 </span>                :     else
<span class="lineNum">      75 </span>                :     {
<span class="lineNum">      76 </span>                :         
<span class="lineNum">      77 </span>                :         
<span class="lineNum">      78 </span><span class="lineCov">              1 :             if (argc &lt; TOTAL_PARAMS) throw BadUseOfGUI(&quot;Incorrect Parameters. Try aso --help&quot;);</span>
<span class="lineNum">      79 </span><span class="lineCov">              1 :             load_sequence(argv[1], nucSeq);</span>
<span class="lineNum">      80 </span><span class="lineCov">              1 :             DataBase DB(argv[2]);</span>
<span class="lineNum">      81 </span><span class="lineCov">              1 :             DB.get_antivirals(antiviralSet);</span>
<span class="lineNum">      82 </span><span class="lineCov">              1 :             AVIterator BDI(antiviralSet.antivirals);</span>
<span class="lineNum">      83 </span><span class="lineCov">              1 :             PluginAdmin* PA = new PluginAdmin;</span>
<span class="lineNum">      84 </span>                : 
<span class="lineNum">      85 </span><span class="lineCov">              1 :             std::string observations;</span>
<span class="lineNum">      86 </span><span class="lineCov">              1 :             std::string outFileName(argv[5]);</span>
<span class="lineNum">      87 </span><span class="lineCov">              2 :             std::string outFilePath(&quot;../outputs/&quot; + outFileName + &quot;.trp&quot;);</span>
<span class="lineNum">      88 </span>                : 
<span class="lineNum">      89 </span><span class="lineCov">              1 :             std::cout &lt;&lt; &quot;-- Observations for this Ranking?: &quot; &lt;&lt; std::endl;</span>
<span class="lineNum">      90 </span><span class="lineCov">              1 :             std::getline(std::cin, observations);</span>
<span class="lineNum">      91 </span><span class="lineCov">              1 :             O algo;</span>
<span class="lineNum">      92 </span><span class="lineCov">              1 :             CombinationStatus stat;</span>
<span class="lineNum">      93 </span><span class="lineCov">              1 :             EmptyCombinatory c1(&quot;emptyComb&quot;);                        </span>
<span class="lineNum">      94 </span><span class="lineCov">              1 :             c1.combine(antiviralSet.antivirals, &amp;algo, stat);</span>
<span class="lineNum">      95 </span>                : 
<span class="lineNum">      96 </span><span class="lineCov">              1 :             ListCombinatory c2(&quot;listComb&quot;);</span>
<span class="lineNum">      97 </span><span class="lineCov">              1 :             c2.combine(antiviralSet.antivirals, &amp;algo, stat);</span>
<span class="lineNum">      98 </span>                : 
<span class="lineNum">      99 </span><span class="lineCov">              1 :             CombineAll c3(3,3,&quot;allComb&quot;);</span>
<span class="lineNum">     100 </span><span class="lineCov">              1 :             c3.combine(antiviralSet.antivirals, &amp;algo, stat);</span>
<span class="lineNum">     101 </span>                : 
<span class="lineNum">     102 </span><span class="lineCov">              1 :             SeqCombinatorialGroup c4(&quot;seqComb&quot;);</span>
<span class="lineNum">     103 </span><span class="lineCov">              1 :             c4.add_policy(&amp;c1,antiviralSet.antivirals);</span>
<span class="lineNum">     104 </span><span class="lineCov">              1 :             c4.add_policy(&amp;c2,antiviralSet.antivirals);</span>
<span class="lineNum">     105 </span><span class="lineCov">              1 :             c4.combine(antiviralSet.antivirals, &amp;algo, stat);</span>
<span class="lineNum">     106 </span>                : 
<span class="lineNum">     107 </span><span class="lineCov">              1 :             print_sequence(nucSeq);</span>
<span class="lineNum">     108 </span><span class="lineCov">              1 :             std::string info;</span>
<span class="lineNum">     109 </span><span class="lineCov">              1 :             antiviralSet.get_info(info);            </span>
<span class="lineNum">     110 </span><span class="lineCov">              1 :             DB.print_database();</span>
<span class="lineNum">     111 </span><span class="lineCov">              1 :             std::list&lt;std::string&gt; ignored;</span>
<span class="lineNum">     112 </span><span class="lineCov">              1 :             insert_into(ignored, &quot;&quot;);</span>
<span class="lineNum">     113 </span><span class="lineCov">              1 :             DB.ignore_antivirals(ignored);    </span>
<span class="lineNum">     114 </span>                :     
<span class="lineNum">     115 </span><span class="lineCov">              1 :             ParallelCombinatory c5(&quot;paralComb&quot;);</span>
<span class="lineNum">     116 </span><span class="lineCov">              1 :             gui_help(&quot;aso.help&quot;);</span>
<span class="lineNum">     117 </span><span class="lineCov">              1 :             c5.add_policy(&amp;c1,antiviralSet.antivirals,false);</span>
<span class="lineNum">     118 </span><span class="lineCov">              1 :             c5.add_policy(&amp;c2,antiviralSet.antivirals,true);</span>
<span class="lineNum">     119 </span><span class="lineCov">              1 :             c5.combine(antiviralSet.antivirals, &amp;algo, stat);</span>
<span class="lineNum">     120 </span>                : 
<span class="lineNum">     121 </span><span class="lineCov">              1 :             Avs in, out;</span>
<span class="lineNum">     122 </span><span class="lineCov">              1 :             AttribSet ejem;</span>
<span class="lineNum">     123 </span><span class="lineCov">              1 :             filter(in, &quot;class&quot;, cPI, out);                    </span>
<span class="lineNum">     124 </span><span class="lineCov">              1 :             filter_by_group(in,ejem,out);</span>
<span class="lineNum">     125 </span><span class="lineCov">              1 :             MutantDist list;</span>
<span class="lineNum">     126 </span><span class="lineCov">              1 :             antiviralSet.observe_mutants(nucSeq,list);</span>
<span class="lineNum">     127 </span>                : 
<span class="lineNum">     128 </span><span class="lineCov">              1 :             OI* obs2 = new OI;</span>
<span class="lineNum">     129 </span>                :             
<span class="lineNum">     130 </span><span class="lineCov">              2 :             OI* obbs = new OI;</span>
<span class="lineNum">     131 </span><span class="lineCov">              1 :             ObserversGroupObserver&lt;int&gt; OG;</span>
<span class="lineNum">     132 </span><span class="lineCov">              1 :             int r = 5;</span>
<span class="lineNum">     133 </span><span class="lineCov">              1 :             OG.attach(obbs);</span>
<span class="lineNum">     134 </span><span class="lineCov">              1 :             OG.update(&amp;r);</span>
<span class="lineNum">     135 </span><span class="lineCov">              1 :             OG.detach(obbs);</span>
<span class="lineNum">     136 </span>                :             try{
<span class="lineNum">     137 </span><span class="lineCov">              1 :                 OG.detach(obs2);</span>
<span class="lineNum">     138 </span><span class="lineCov">              1 :             }catch (...){}</span>
<span class="lineNum">     139 </span>                : 
<span class="lineNum">     140 </span>                : 
<span class="lineNum">     141 </span><span class="lineCov">              1 :             if (PA-&gt;load_plugin(&quot;thesis_plugin.so&quot;))</span>
<span class="lineNum">     142 </span>                :             {
<span class="lineNum">     143 </span><span class="lineCov">              1 :                 AntiviralsNames rejectedAntivirals;</span>
<span class="lineNum">     144 </span>                : 
<span class="lineNum">     145 </span><span class="lineCov">              1 :                 if (!PA-&gt;check_plugin(BDI, rejectedAntivirals))</span>
<span class="lineNum">     146 </span>                :                 {
<span class="lineNum">     147 </span>                :                     //std::cerr &lt;&lt; &quot;Error: plugin and Data Base incomplatibles.&quot; &lt;&lt; std::endl;
<span class="lineNum">     148 </span>                :                 }
<span class="lineNum">     149 </span>                :                 else
<span class="lineNum">     150 </span>                :                 {
<span class="lineNum">     151 </span><span class="lineCov">              1 :                     TherapyRanker rankerObs(atoi(argv[3]));</span>
<span class="lineNum">     152 </span>                : 
<span class="lineNum">     153 </span><span class="lineCov">              1 :                     ParameterList params;                     //! Inicialización de parametros</span>
<span class="lineNum">     154 </span><span class="lineCov">              1 :                     PA-&gt;get_params(params);</span>
<span class="lineNum">     155 </span><span class="lineCov">              1 :                     gui_plugin(params);</span>
<span class="lineNum">     156 </span><span class="lineCov">              1 :                     delete_container(params);</span>
<span class="lineNum">     157 </span>                : 
<span class="lineNum">     158 </span><span class="lineCov">              1 :                     TherapyGenImpl G(rankerObs.get_observer(), antiviralSet, PA);</span>
<span class="lineNum">     159 </span><span class="lineCov">              1 :                     G.generateTherapies(nucSeq);</span>
<span class="lineNum">     160 </span><span class="lineCov">              1 :                     gui_print_ranking(rankerObs, outFilePath, observations);</span>
<span class="lineNum">     161 </span><span class="lineCov">              1 :                     std::cout &lt;&lt; &quot;Ranking created at: &quot; &lt;&lt; outFilePath &lt;&lt; std::endl;</span>
<span class="lineNum">     162 </span>                :                 }
<span class="lineNum">     163 </span><span class="lineCov">              1 :                 PA-&gt;unload_plugin();</span>
<span class="lineNum">     164 </span>                :             }
<span class="lineNum">     165 </span>                :             else
<span class="lineNum">     166 </span>                :             {}
<span class="lineNum">     167 </span>                :                 //std::cerr &lt;&lt; &quot;Cannot load plugin&quot; &lt;&lt; std::endl;
<span class="lineNum">     168 </span><span class="lineCov">              1 :             delete PA;</span>
<span class="lineNum">     169 </span>                :         
<span class="lineNum">     170 </span>                :     }
<span class="lineNum">     171 </span><span class="lineCov">              1 :     BadUseOfGUI aa(&quot;a&quot;);</span>
<span class="lineNum">     172 </span><span class="lineCov">              1 :     aa.what();</span>
<span class="lineNum">     173 </span><span class="lineCov">              1 :     BadValue b(&quot;b&quot;);</span>
<span class="lineNum">     174 </span><span class="lineCov">              1 :     b.what();</span>
<span class="lineNum">     175 </span><span class="lineCov">              1 :     SystemError c(&quot;b&quot;);</span>
<span class="lineNum">     176 </span><span class="lineCov">              1 :     c.what();</span>
<span class="lineNum">     177 </span><span class="lineCov">              1 :     PluginError d(&quot;d&quot;);</span>
<span class="lineNum">     178 </span><span class="lineCov">              1 :     d.what();</span>
<a name="179"><span class="lineNum">     179 </span>                :     </a>
<span class="lineNum">     180 </span><span class="lineCov">              1 :     return 0;</span>
<span class="lineNum">     181 </span><span class="lineCov">              3 : }</span>
</pre>
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